The freshwater fishes of Turkey have been studied for more than 150 yr. However, a nation-wide inventory of freshwater fish occurrences in all transboundary river basins (Euphrates–Tigris, Coruh, Kura–Araks, Maritsa and Orontes) has been neither studied nor published. This work is the first extensive study of the composition and biological characteristics of the freshwater fish fauna of the transboundary rivers in Turkey, with special reference to the native and non-native status of species, and the spatial patterns of species e.g., abundance category, endemism, main threats, movement patterns, habitat guild, feeding guild, and reproductive guild. It is determined that a total of 184 fish species in 25 families (including 15 species which are not native, and 30 species are considered as endemic) live in the transboundary river basins in Turkey. Of the 184 fish species: 19 species are abundant, 57 species decrease, and 101 species are data deficient based on IUCN Red List (International Union for Conservation of Nature and Natural Resources). One of the main threats to freshwater fish occurrences in all transboundary river basins are dams. Most fish species in the area are threatened by dams, water extraction, and habitat degradation.